Time Lord Instincts
by Chasingthestars123
Summary: The Doctor is a lone Alpha, traveling the stars with many companions but never with the right Until one day he finds Clara Oswald who jumps into his time stream, getting ripped into The Doctor manages to get her out alive but she brought something with her, the scent of an Omega Time The Doctor's instincts can't resist Can he claim her before it's too late?
1. Chapter 1

There are many rules when it comes to Time Lords.

Respecting elders and following orders are some of the rules that Galliferyians must obey, but only when it comes to breeding do the rules change.

There are ranks within the Time Lords that are not spoken upon but rather known by instinct when born. Each Time Lord gives off a certain scent that indicates what rank he or she holds; Alpha, Beta, or Omega.

The Alphas are the stronger, more powerful ones and holds a higher rank than others. They are dominating and territorial when it comes to their mates and can be very aggressive and possessive when their mate is in heat. Their first priority is to make sure that their mate/partner or family is safe under their protection. Alphas only mate with Omegas and when they do they rely only on instinct which is to fill his Omega's needs by knotting and impregnating her. The Alpha knots when both partners are on the verge of orgasm and the base of his cock swells up, preventing him from pulling out and pouring all of his seed into his female, impregnating her. Knotting only occurs when both mates are bonding during heat, once the Alpha Male knots then they are mates for life. An Alpha holds a lot of semen to ensure that his female is pregnant during heat, if the Alpha does not join his Omega in heat then she will go through that period of intense pain and arousal until it's over(which may take from a few days to weeks). Time Lords, especially Alphas, can immediately smell when their mate is in heat and can mark them by rubbing their scent on them or biting them. Alphas do not and cannot mate with Betas.

The Betas are like your normal everyday people who do regular people things. Betas don't mate with either Alphas or Omegas simply because they can't. It's against the rules for a Beta to mate especially with an Omega, they first must be of a higher ranking(Alpha). If a Beta were to mate with an Omega(or an Alpha) they would be shunned and thrown down to the rank of Omega.

The Omegas are the lowest of the low in the ranks and are looked down upon. They are usually submissive to anyone of higher rank and are genuinely caring. They periodically go into heat and they can't go through it alone without an Alpha to fulfill her needs. An Omega can get pregnant and can bear children only from an Alpha, not a Beta. For a bond to be complete, the Omega must agree to the relationship she has with her mate and participate in the mating process. The Omega must always be submissive towards her mate whether it's during heat or not simply because it's part of their DNA and instinct to submit in any way.

The Doctor couldn't help by thinking of these ancient rules as he carried Clara out of his time stream and into the dead TARDIS. While he was searching for her in his God forsaken tomb, he had managed to catch the scent he thought he would never smell again. The scent of a Time Lady. An Omega Time Lady. He had tilted his head back in the air and sniffed. And she was fertile. He had felt his body react to such a scent but quickly refocused on finding and saving Clara, but he found that as he drew nearer to her the scent grew stronger and it caused his instincts surface. The Doctor knew that the scent shouldn't affect him this strongly but he hasn't smelled it in over hundreds years and it was making him very hungry for touch and intimacy. The Doctor isn't sure how Clara could've picked up the scent of a Time Lady, but he pushed the thoughts down along with his instincts and quickly gathered her up, leaving his time stream and his greatest secret behind.

As soon as he stumbled out, Vastra, Jenny, and Strax were there to help him back to his TARDIS. Strax had offered to carry Clara for him but the Doctor declined, clutching her closer and inhaling her scent. During their journey back, the Doctor had thought how it was possible that Clara had picked up the alluring smell of a Time Lady even when she is one hundred percent human. At least she was the last time he'd checked. Unless one of her echoes landed on Gallifrey. No, he thought, it's not possible. It couldn't be yet here she was in his arms, his nose practically buried in her neck.

Once they stumbled into the TARDIS, the Doctor immediately set the coordinates for the three detectives' home, still not letting go of Clara making the process much more difficult. Vastra and Jenny offered to help many times but the Doctor refused, telling them they should head home before another disaster occurs, no pun intended. They all left reluctantly leaving the Doctor to steer the TARDIS into space and to carry Clara into his bedroom where he laid her down, pulled the covers over her and sat next to her on a chair he grabbed from the corner. All the while pondering over the idea of Clara as a Time Lady. He watched as her chest moved up and down and how her eyes moved under their lids, he caught a rebellious strand of hair and softly pushed it behind her ear. He leaned forward and inhaled deeply, humming in content at her scent.

He then laid an arm around her waist, pulling her closer to him. He flipped out the Sonic and scanned her body before reading the results: Time Lady. The Doctor's eyes widened and looked down at his impossible girl who has been ripped to a thousand shreds, echoes of her dying over and over again just for him. He owes her everything now. But he still can't believe it. Clara, his Clara, a Time Lady. She has seen everything he has done, knows about his darkest days, the things he had done that he wishes he could take back. And now she has seen his planet, his home. She has lived a life there with him, even though he doesn't remember seeing her. Oh, Clara, my Clara, he thought, Mine.

His head shot up. Did he just say Clara was his? No, Clara wasn't his. She was never his. But his instincts thought differently as he caught some more of her scent in his nose which triggered a part of his brain that let out the Alpha in him. No. Must not let it out. Clara literally just got back from dying a thousand times you can't just claim her like that! Yes, you can. No! Yes, do it, you're an Alpha you can claim and Omega like her. No! Stop!

The Doctor shook his head to get the thoughts out of his head. He would not let his instincts get the better of him.

As he rests his head against her chest and breathes in her scent, he vows he will do whatever it takes to make his Impossible Girl safe under his protection.


	2. Waking Up

**Author's Note: Hey guys, thanks a lot for the positive reviews I've been getting! You guys are really supportive in helping me write this story! I just wanted to say that the rating will defiantly change over the course of the story I just forgot to mention it in the first chapter.**

**Doctor Who doesn't belong to me it belongs to the BBC.**

**Thanks again!**

**Enjoy!**

It's been a week since the Doctor and Clara left Trenzalore and Clara was still hasn't woken up. The Doctor has tried everything to wake her up, anything to make sure she was okay, but got nothing. All he can do right now is to sit next to her in hope that she would wake soon.

During the time she was unconscious the Doctor would read stories to her from books he quickly got from the Library, would tell her of his past companions(though he thinks she already knows about them by now), and even sing to her old Gallifreyan lullabies in his mother tongue to soothe her whenever she had nightmares.

The Doctor thought about holding her in his arms but found it too dangerous since his instincts were still present. Though they were steady now, he's afraid that if he gets any closer to her his instincts would take over and he defiantly didn't want to scare Clara away, if she would wake up that is. Still, he didn't want her to wake up and ask why she was covered head to toe in his scent. Though the thought is very tempting he would not allow himself to do such a thing, he was better than that!

The Doctor shook his head once again to relieve the thoughts, pushed up his glasses, and went back to reading Hitchhiker's Guide to the Galaxy to Clara.

A month has passed and there was still no sign of Clara waking up. The Doctor was starting to think that she was never going to wake up. He was sitting on the same chair he's been sitting on for the last month, elbows rested on his knees, head buried in his hands, maybe the universe doesn't make bargains after all. His tried, old eyes started to water, he squeezed then shut and hung his head. After all the adventures they've had together, it was such a short time. It wasn't fair. It was never fair. Yet, here he was losing another companion, another friend, another piece of his hearts.

He got up and walked around the bed towards the door to go fetch another book from the Library when his sharp ears heard the faint noise of rustling sheets from behind him. He quickly spun around and sprinted the short distance to the bed, sitting on the bed he grabbed her hand, running his thumb over the smooth, silky skin. His other hand reached up to run through her hair, gently palming her face. Green eyes looked down hopefully at Clara as she stirred under the sheets.

"Clara, can you hear me? Clara?" He asked, voice full of heavy emotion.

Clara's head rolled from side to side exposing her neck to him. The neck was were one of the main scent glands that were on the body of a Time Lady, causing the Doctor to inhale deeply and lean forward, nose brushing her throat. The Doctor had to rip his hand from Clara's to clench his fist, nail digging into his skin. He had to get these instincts under control, it was getting out of hand. How was he supposed to tell Clara that he had to urge to claim her body once she woke up? He can't! Unless you want a very awkward conversation with the Doctor telling Clara about the bird and the bees of Time Lords.

Simply explaining to Clara about the mating habits of Time Lords was going to be very difficult enough, Time Lords(and Time Ladies)know about their mating process and rank instinctively when their born( A Gallifreyans' growth rate is faster than a humans). There's no embarrassing talk with your parents about why you have wet dreams on Gallifrey because you already knew why. He wondered if Clara would know about this when she woke up, which was now.

Clara's eyes fluttered open.

"Doctor?" She asked with her sleep deprived voice.

The Doctor forced himself back to the present and looked down at her with worried eyes. He grabbed her hand again.

"Hello," He smiled softly.

"Hello" She smiled back. His eyes shot down to her lips then back to her face. No, don't think those thoughts! Bad Doctor!

"How are you feeling?" He ran his thumb over her brow and sighed.

"Like I've been run over by a thousand buses."

He chuckled softly and brought his forehead down to hers. He slid down beside her into a more comfortable position and wrapped his arms around her waist, pulling her closer.

"Do you remember anything?" He sighed.

"Not much. It's like a dream sort of," She looked up at him,"I remember it, but it fades."

The Doctor nodded. Then he inhaled again.

"Do you remember anything about Gallifrey?" He asked quietly. He's already assumed she'd been there as an echo, why else wouldn't she be covered in Omega sent?

Clara was silent for a few moments before she met his eyes.

"A little, yes,"

"How much?"

She paused.

"I remember the red grass, the silver trees, and the snowcapped mountains," The Doctor closed his eyes.

"And something else I can't really explain," She said, her eyes in a daze.

"Like what?" The Doctor asked, though he probably knew what it was.

"I don't know, its like," She paused, "Something's there in my mind and I'm not sure what it is." She said.

"Is it a nagging feeling?" He asked.

Clara nodded slowly.

"Yeah," Her brow furrowed, "How did you know that?"

"Just a gut feeling," He said.

Clara eyed him suspiciously, but sleep was tugging at her. She yawned and the Doctor adjusted the covers on her, though he stayed in the same spot next to Clara. Need to make sure my mate feels protected and comfortable. He snarled mentally. Clara is not your mate! Stop it! You haven't even claimed her yet! Let alone tell her you have feelings for her!

He growled.

Clara looked at him curiously.

"Is something wrong?" She asked.

The Doctor immediately smiled softly, trying to cover up.

"No, no, everything's just fine, I just," He paused, "Have heartburn." He pounded his chest with his fist, fake coughing.

Clara rolled her eyes and turned so she was facing away from him.

"Alright," She snuggled into the warm blanket.

The Doctor coiled his arm around her waist and pulled her to him, ignoring his instincts and thoughts.

After about twenty minutes when the Doctor thought Clara was sleeping, he moved his head closer to her neck and sniffed. He sighed in pleasure and smelled again. He did this a few more times before he needed more. He inched closer to her and buried his nose behind her ear, nuzzling in her warmth. His grip around her waist tightened as he started pressing open mouth kisses on the sensitive shell of her ear. He hadn't noticed that Clara had gone still under his touch, but continued his actions without caring. He nibbled along her earlobe, teeth chewing the delicious flesh, his tongue flicking out to taste.

He bit back a moan as he sucked on her flesh, he couldn't help himself, and his instincts demanded it.

He was oblivious to the fact that Clara was still awake and could feel and hear everything. She was confused and afraid, she wasn't sure what was going on. She had to keep herself from whimpering when he started to nibble on her ear. She almost cried out when he sank his teeth into her earlobe, she bit her lip and froze. She wasn't sure why but she felt awfully submissive to him, like she wanted to please him, it was her job, instinct. But she didn't want to move in fear of ruining the moment so she just stayed still and waited until he was finished.

The Doctor only pulled her closer and growled softly into her ear, wrapping his leg possessively around her's.

"Mine," He murmured.

His tongue darted out to taste her more. He ran his tongue over the sensitive skin behind her ear, his warm muscle leaving a wet trail behind it as it continued to make its way down her neck and along her jawline. He thought he heard a whimper but shrugged it off and continued to lick down her throat.

Clara just stayed like that, letting him explore her neck and throat until he grew tired and eventually fell asleep, body curled protectively around her and face nuzzled in her neck. She too soon fell asleep but not for long as thoughts kept plaguing her mind about what the whole incident was about with the Doctor. She looked at the alarm clock next to the bed and realized it was too early to wake up yet and tried to fall asleep. In the morning, well there technically is no morning on the TARDIS, she would ask him about what he did the night before.

And it sure would be the most embarrassing conversation she would ever have with him.

**Author's Note: Hey guys! I'm glad you enjoyed that little chapter there! I know its short but it's hard when you have to share the computer with your little brother every hour and a half during the day. **

**I'm not sure when I'll be able to update since school is tomorrow and I have a ton of High School homework but I hope you'll keep a look out for new chapters.**

**Maybe I'll upload a new chapter every week end or something I'm still not sure.**

**Until then guys! :{ - Chasingthestars123**


	3. Chapter 3

Eyes opened groggily as Clara began to awaken. She stirred and lifted her head to peer around the bed room. The TARDIS programed holographic light into the nearby window to brighten up the room, making Clara squint her eyes a little.

She tried to sit up but quickly found out she was trapped by a pair of strong arms wrapped around her. She looked down to see the Doctor curled protectively against her body, his possessive leg still tangled in her own. She tried to move them, only to have it tighten around her legs. She sighed in defeat and glanced down at the peaceful face of the Time Lord next to her.

She was confused as to why she was in his bedroom when it all came back to her. Her eyes widened as she remembered what the Doctor did last night, her face went a deep shade of red. They were going to have a serious (and embarrassing) talk once he woke up, one that she really wasn't looking forward to at all.

What were the cause of his actions? He'd never acted like that before. She checked again. Nope, not ever. So what could it possibly be? She didn't know, yet she kind of liked what he did. Did she just say she liked it? Yes, but why? Clara stared in confusion at some wall when she felt the Doctor shift, burying his face deeper into the crook of her neck.

She then caught a whiff of something, it smelled…sweet. She looked for the source and found her nose bumping against the Doctor's jaw. Has he always smelled this good? She hasn't recalled a time where he gave off such an alluring scent. Her cheek hit his chin as she nuzzled his neck.

Then something went off in her brain, like some sort of trigger. She lifted her head in confusion when there was a word in her mind, she's heard it before, but where? It was almost as if it was alerting her of something: Alpha. What does that even mean? It was like her brain was telling her there was an Alpha nearby. What's an Alpha?

She was in the middle of thinking when she felt the Doctor stir, he lifted his head and looked at her with sleepy, confused eyes. He looked down to see his body tangled in hers and his face blushed a bright red. He awkwardly freed their limbs from each other and moved his body away from Clara, avoiding her gaze. The air so was tense Clara felt like she was suffocating from the awkwardness in the small room.

They sat there for a few moments, gazing around the room, not daring to look at each other. The Doctor began to fidget with his hands and Clara played with the hem of her shirt. The Doctor dared a glance at her and opened his mouth but slowly closed it, like a flustered fish and went back to ringing his hands.

Clara couldn't take it any longer and finally broke the ice. She took a deep breath, causing the Doctor to look her way.

"So," She looked at him.

The Doctor waited for her to continue.

"I've been meaning to talk to you about something."

He nodded.

"Is something wrong?" He asked, worry stretched on his face.

"No, well, I…I don't know," She answered.

He was about to respond when Clara suddenly spoke.

"What happened last night?" She blurted.

The Doctor's lips straightened into a thin line.

"Well, we talked about your echoes and Gallifrey-''

"No, I mean after that."

"After that?" He gulped. She wasn't awake was she? Oh, Rassilon, he prayed to all the Gods that she wasn't.

"You know, when you started to," She motioned awkwardly with her hands, "Do things."

"Things?"

"You know what I mean,"

God, this was so embarrassing. The Doctor looked down and began to fiddle with his hands again.

"Ah, yes, um, well, you see," He scratched his face, "Do you remember the ranks on Gallifrey?"

Her brow furrowed in confusion.

"The what?"

The Doctor sighed. This was going to be a very long conversation. He swallowed thickly. He spoke, voice low.

"Well, back on Gallifrey there were three types of ranks: Alpha, Beta, and Omega."

Clara listened, intrigued by what he was saying.

"These ranks helped us manage our society, sort of like how your people have government ranking, but it's nothing like that. The Alphas are the stronger ranking, they're more powerful and are considered leaders of groups, there are capable of dominating others of lower value." He paused.

"Sounds like they're not to be messed with," Clara said.

"Yeah, anyway, after the Alphas are the Betas and they are not really noticed that often. They are like your normal person doing everyday normal things. Other than serving and watching over the young they're practically ignored."

"That sounds mean. Why?"

"Well, they are not really useful to the Alphas and I guess since they are also useless to Omegas, we don't think we need them. But since the Beta is higher than an Omega it gives the feeling of pride and accomplishment to whoever moved up."

"But, still, I wouldn't ignore someone who looks over my children. In fact I think they should be the most respected in the ranks." Clara said.

"It's very complicated and hard to explain. And finally the Omegas, they are the lowest rank of all. They are very kind and careful with others and are submissive to anyone of higher rank. Their purpose is to serve the Alphas and sometimes if the Beta isn't available they would watch the young. They are very useful to Alphas and can become a Beta if an Alpha were to promote them, so to say." He said.

"How are the Omegas useful to the Alphas if they're the lowest in rank?" Clara asked.

The Doctor looked away.

"Well, an Omega is capable of becoming an Alpha's mate." He said.

"Mate. You mean like lover?" She asked.

"Sort of, but it's different. If an Alpha wanted to claim an Omega for a mate he could because he's of higher rank. The Omega would have to agree to their relationship before they were to, you know," He gestured to Clara.

"Mate?"

"Yes, an Alpha can claim an Omega, but an Omega can't claim an Alpha. You see?" He asked.

"Sort of, but what does this have to do with last night?" She asked.

The Doctor's face blushed red again.

"Well, you see, I'm…uh, I'm an Alpha," He said quickly.

"You are? You always seem to caring and gentle, not like how you described Alphas."

"I know, I try not to be like them." Anger flashed in his eyes, but it was gone in a second.

"So, you're an Alpha," She continued.

"Yes, and you're an Omega," He looked at her with what Clara thought was lust before it disappeared. She tried to piece the puzzle together in her head.

"How can you tell what rank I am?"

"I can smell it. Every Time Lord, or Lady, has his or her own scent that gives off what they are, they are born with that rank and will instinctively know it until they move up a rank." He said.

"Okay, but I'm still confused about last night," She looked at him in confusion.

He sighed again and scratched the back of his neck.

"You give off the scent of an Omega Time Lady, which I haven't smelled in over a hundred years and it's driving my instincts absolutely mad. I'm afraid that if I get too close I'll scare you or worse, drive you away. Last night I let my instincts control me which I shouldn't have done. What I did was very inappropriate, so I'm sorry if I made you uncomfortable and I understand if you want to leave." The Doctor hung his head, preparing himself for the yelling and cursing he would get.

But it never came.

Clara giggled and the Doctor looked up.

"What's so funny?"

She smiled up at him, which made his hearts leap in his chest.

"Doctor, I'm not mad."

"You're not?" He asked, confused.

"No, it's alright if you have a crush on me," She gave him a kind grin.

The Doctor flustered, face turning bright red.

"No, that's…that's not, erm….um, I- shut up!" He turned away.

Clara chuckled again.

They both sat silently until Clara spoke up again.

"You know," She started.

The Doctor looked up.

"I have this rule I made where if I start to have humany-wumany feelings for you" He smiled at her use of words, "I would tell myself to not fall for you because I know it could never happen." She said sadly.

The Doctor stared at her for a few moments, still smiling softly.

"Then maybe you should stop,"

She glanced at him.

"The rule, I mean, to, you know, stop telling yourself to stop falling in love," He said awkwardly, causing Clara to laugh again.

"So when did we become a bit flirtatious all of a sudden?" She asked cheekily.

"Whenever I see that gorgeous face of yours," Now it was her turn to blush.

"Now you're just being corny," She giggled.

The Doctor laughed along with her. He gazed in her doe-like eyes and found himself in a daze, subconsciously leaning forward. Clara noticed and smirked, leaning forward as well until their foreheads bumped. The Doctor's green eyes stared longingly into hers as he leaned closer, their lips almost touching. Clara raised an arm and slowly started caressing the soft, brown locks on the back of his neck gently, liking the feeling they made against her fingers. His eyes closed and he began to purr. Her eyes widened at the animalistic sound.

"Doctor, are you purring?" She asked and continued to stroke.

"Hmm? Oh, yes it feels good," He mumbled, stretching his neck so she can get more access to his hair.

She giggled as he nuzzled her hand for more, fingers treading through his scalp. His arms wrapped around her waist and pulling her closer, he moved his head to burry in her neck, inhaling. Clara sighed in pleasure, clutching his head tighter and pressing her lips to his temple, causing him roll in her under him with surprising strength. She gasped but was cut off when his lips crashed onto hers, moaning as she kissed back, lips moving together in sync. His arms circled completely and pulled her body off the bed and flush against him, lips leaving her mouth to trail down her jaw to her neck. She whimpered when she felt his teeth nipping her silky flesh.

"Doctor," She cried.

He growled lowly, pushing her deep into the bed, both knees on either side trapping her. He grabbed both hands and pinned them against the sheets. She felt her instincts start to kick in and she exposed herself, submitting to him, giving him her body, letting him claim her. He rumbled in satisfaction, finally after all these hundreds of years he was going to have a mate again. It gave him pleasure to see his mate so ready for him to take. He felt his Alpha start to rise and he gladly accepted it, getting ready to claim, to dominate. He rolled his hips against hers, feeling himself get hard. Clara gasped at his hardness and jerked back from him. The Doctor's eyes furrowed in confusion.

"What's wrong? Did I hurt you?" He asked, concern and worry on his face.

"No, it's just I don't want us to move too fast," She said.

"Of course, right, sorry-"

"Don't apologize, Doctor. I liked it," She said shyly.

"You did?" He smiled.

The Doctor, though it was hard, pushed his instincts back down and sat up.

"Yes," She yawned.

"Alright, then. Did I tire you out already?" He teased.

"Shut up," She smiled, "No, my head hurts from all of the memories." She grimaced and held her head.

The Doctor quickly got off her and carefully laid her down onto the bed. He sat down next to her and stroked her hair as she closed her eyes, breathing softly. He laid a kiss on her forehead.

"Get plenty of sleep. We'll figure out what to do in the morning, love." He said.

Then he realized what he just said and froze. He looked down to see Clara sleeping and sighed in relief, turning around and walking towards the door. He looked back one last time before he stepped out and closed the door behind him.

**Author's note: Hey guys! Sorry the ending is crappy, I ran out of room in Microsoft Word and I don't know how to open new pages. Help!**

**Anyway do expect another chapter until next week, I think.**

**Plus, everyone in my family suddenly wants to use the computer once I'm on it so it takes me a while to write these chapters.**

**So, see you next week! I hope!**

- **:{ Chasingthestars123**


	4. Chapter 4

"So, what do we do about the echoes and memories?"

Clara was leaning against the console, watching the Doctor spin and skip around like the man-child he was. She had woken up with another nightmare and the Doctor had to lay down on the bed and comfort her, telling her he was there. They had both eaten breakfast and were now chatting, the Doctor stealing a kiss every few minutes. He still blushed whenever he did but that was the Doctor.

"Well," He spun around to face her, "Since you're a Time Lady now your brain should be able to sort them out, otherwise you'll be fine. Though, you might have a few nightmares every once and a while, but that's just your brain doing its job."

Clara nodded and strode towards him, resting both hands on either side of his hearts. He looked down, eyes shining a dark green.

"So, where to?" She asked.

The Doctor's eyes widened and he took her hands in his.

"Oh, you're not going anywhere, Miss Clara."

Clara rolled her eyes.

"You said it yourself, I'll be fine," She said.

The Doctor spun around once more before running around the console and flipping switches.

"Yes, but your brain needs time to sort everything out and the only way for it to do that is to rest. Which means you'll be staying here for the next few days. Week maybe, or more." He said.

Clara followed him.

"You'd like that now, would you? Keeping me with you at all times, not letting me leave? Are you up to something?" She smirked.

His own lips started to curl.

"Maybe," He leaned forward, "What are you going to do about it?"

She leaned closer as well.

"I have a few things in mind," She teased.

She placed one hand on his chest and the other on the back of his neck, caressing his brown hair. His arms wrapped around her pulling her closer, he inhaled her scent.

"Oh, really?" He growled softly, their noses rubbed against each other.

"Yes," She whispered.

"And I'd like to start," She ran her hands over his chest making the Doctor's back stiff with pleasure.

"In the Library." With that she spun around and walked up the small flight of stairs and into the corridor, leaving the Doctor stunned and confused.

Clara looked over her shoulder and winked, an obvious sign for him to follow her. And he got the message just fine. He sprinted up the stairs after Clara, reaching out for her, but she slid from his grasp and broke into a run towards what she hoped was the Library. Know the Doctor loved a good challenge, she skid and ran through many corridors all the while looking for the place she wanted to relax. Apparently, the TARDIS wasn't on her side as she saw the Doctor coming at her full speed from beside her. She didn't have enough time to get away when he snatched her arm and yank (not roughly, never roughly) her to him, wrapping his arm securely around her and determined to not let her go. She yelped when he held her from behind and giggled when he lifted her into the air slightly.

He growled playfully into her ear and nuzzled his head between her neck and shoulder, he just couldn't get enough of her sweet smelling scent. It was intoxicating, making him burry his head deeper and holding her even tighter if it was possible. Her giggles died down and she sighed, bringing her hand up to run her fingers through his hair and resting her cheek on his temple. He purred and closed his eyes, savoring the moment of having her in his arms. After all this time of being with her, having adventures together and sharing wonderful moments with her he finally gets to just holder, have her. As his.

Well, not yet. He still has to bond her with him. And mark her as his. He rumbled greatly at the thought of making Clara his permanently. Having her as his mate, she would belong to him and him alone, no one else. He took great satisfaction at having Clara. Of course he would have to wait until she goes into heat, which he didn't know when that would be. He wanted it to be soon, he couldn't wait any longer yet he didn't want to ask Clara, that would be too embarrassing and would look suspicious.

It just occurred to him that Clara had never been in heat before, she wouldn't know what to do. She would probably be confused and afraid, sitting on her bed with soaked thighs, whimpering, whining, and begging for her Alpha to take her. She would be in an intense state of arousal and pain, just waiting to be claimed, her Omega instincts making her submissive and open for _him…_

He hadn't realized he had been pinning Clara to the wall, his eyes nearly black with hints of dark green sending a predatory gaze at her. His breathes are deep and hot, his arms on either side of her, trapping her between himself and the wall she's pressed to. Her eyes, irresistible yet innocent, looked straight into his eyes. She looked confused, but he could smell her arousal lingering through the air, making his pupils dilate and upper lip curl into a small snarl and bared his teeth.

Clara's Omega instincts kicked in, making her submit to the powerful Alpha male standing above her. She shifted her head and allowed him more access to her neck for scenting which the Doctor very much obliged to, lowering his head to get a good whiff of her smell, which made him shiver in delight. Clara could feel the Doctor's hard member digging into her stomach and shrunk back, suddenly feeling unsure and unprepared. She whimpered slightly but not in pleasure.

The Doctor noticed her discomfort and immediately backed away, looking confused and worried at her sudden behavior. He raised her head with his hand and looked into her eyes.

"Clara, is everything alright?" He asked.

Clara felt abruptly felt insecure and her little body shrivel even more.

"I don't know, I… I just don't feel like I'm ready yet, to, you know," She gestured, "To do this."

The Doctor sensed her panic and held her shoulders with comforting hands, rubbing them up and down her arms.

"Hey, it's okay. We're not in any hurry here," _Well, at least you're not anyway, _He thought.

"You can take all the time you need, alright. I promise I'll be right here by your side," He said. _Waiting._

He watched as Clara took a deep breath and looked up at him.

"Let's just go to the Library," She smiled softly.

The Doctor smiled back and nodded.

"Of course," He led her towards the Library, still holding her shoulders for reassurance.

On the way, the Doctor had to try and suppress his Alpha instincts and his hard member which was one of the hardest things her had to do in his entire life, especially when there's a fertile Omega not a few inches from him.

But none the less he would wait for her, he didn't want to come off as too forceful or impatient and scare her away.

I took a couple of corridors and a few doors but they finally reached the Library and Clara sighed in relief. She headed off to the non-fiction section with the Doctor not far behind, curious as to what she's looking for. She skimmed the isles, her eyes hunting for a certain book somewhere in the 'G' section, until she found it. The Doctor's eyes widened when he found out what book she was looking for: _The Encyclopedia of Gallifrey._

The book held everything about Gallifrey, including its wildlife, native plants, Gillfreyians, and even the reproduction cycle of the Time handled the ancient book with care and walked over to the loveseat in the living area of the giant library. Without a word she sat down and set the book down on the coffee table in front of the seat while the Doctor sat next to her, waiting for her.

Clara stared the book down and carefully opened the dark brown, thick cover.

"The language of Gallifrey was so beautiful, but I forgot it." She said, "It's somewhere in my head, I know it. But no matter what I just can't remember."

The Doctor sat silent for a moment.

"I could teach you," He looked up at her.

Clara smiled at him, and he loved seeing her smile.

"Thank you, Doctor," She kissed him on the cheek and he closed his eyes, sighing.

She turned the page and scanned down the contents until she came across _The Mating Habits of Time Lords_ and smirked at him. The Doctor's face turned a bright red and was inwardly begging Clara not to turn to that page. It's not a topic he finds comfortable talking about._ Clara, don't turn to that page! Damnit._

The Doctor shot up from the seat, making Clara jump.

"I'm just gonna go….fix something. You know the TARDIS, always needs fixing!" He quickly ran from the Library, making Clara giggle.

She turned back to the book and flipped through the old, withered pages.

Sitting alone in the console room gave the Doctor some time to think about what has happened in the last few days. But mostly to think about Clara.

He sat down on his hammock underneath the control panel with his goggles strapped to his forehead and sonic in hand, grabbing a handful of wires and fixing something that probably doesn't need any fixing. He let his mind wonder to Clara and how she changed him when she walked right into his life without knocking. She made him look at the world in a different way, something that many cannot do, even his closest friends and gave him the feeling of falling in love all over again. He loved the way her brown hair was so incredibly soft, how her silky skin felt against his rough hands, the way he runs his fingers over her lovely curves, the sharp pleasurable sensation he gets when he inhales her scent deeply. Her Omega scent.

He shivers violently when he remembers the sweet smell of her, especially that one section behind her ear which is the main scent gland (He loves burying his face into that spot). Even though he absolutely _loves _how she smells, there is just one thing that bothers him. That _really _bothers him. She doesn't smell like him. During the mating ritual when the Alpha and Omega are planned mates, it's the Alpha's job to make sure that everyone is to know that the Omega is his and his alone to make his mate feel protected, and a traditional way to do that is to cover her head to toe in his scent. Without his scent to mask her own she smells unclaimed and that makes him feel very uncomfortable because that means he's not doing his job. And when he's not doing his job it makes him feel overprotective and possessive of her, trying to keep her his for as long as possible until her next heat cycle, which could be next month for all he knew.

The main scent glands on the Alpha are on his hands, neck, chest and genitals, and he plans on using all of these very soon. The urge to claim Clara gets stronger every day, his Alpha male instincts to possess her grow more aggressive every time he smells her scent. He can't help it, it's his instinct that tells him he has to have Clara, he has to own her, claim her, and make her his mate forever. He has been touching Clara a lot more than before to get as much of his scent on her as possible without her noticing, it probably won't get by her because she can smell him just as much as he can smell her.

By the time he had finished 'fixing' a part of the TARDIS, Clara had come from behind him and wrapped her arms around his neck, kissing his neck lightly. He hummed in return and turned to nuzzle his face into that spot behind her ear, inhaling deeply before darting his tongue out to taste her skin making her sigh and stretch her neck for him to get more access to.

"I was just thinking about you," He said between open mouthed kisses on her neck.

Clara sighed once more.

"Hmm, were you?" She asked hand coming up to stroke a certain place on the Doctor's scalp.

"Yes, I was," He gasped when he felt her hand massage that part of his head and immediately started purring.

Clara giggle at the cat-like sound emitting from him and watched as he practically melted into her arms, nudging his face against her and his hands grasping her waist.

"Where did you learn that where that sensitive part on my head was?" The Doctor moaned.

Clara smirked.

"From that helpful Time Lord book of yours from the Library,"

He blushed a dark red.

"Oh yes, that book," He began to rub his hands up and down her body.

"Doctor, I've noticed how you keep touching me,"

He pretended to act confused.

"I always touch you, Clara. What are you talking about?" He asked.

She put her hands on his arms.

"You know what I'm talking about. You've been trying to mark me by coating me in your scent," She said.

He looked up at her.

"Now, Clara I would never do that," She gave him a look.

"I wouldn't!"

"Doctor, I can smell it,"

The Doctor slumped in defeat.

"Fine, I was. I just… I feel the need to claim you but I don't want to scare you away because you haven't reached your first heat yet and-"Clara cut him off with a kiss which he immediately kissed back. She backed away.

"Doctor, I'm not going to be scared because of something you can't control. Plus, it would be fun messing around with you for the next few weeks," She grinned cheekily.

The Doctor gave her a warning growl.

"Now, Clara I wouldn't recommend doing that to an Alpha male Time Lord,"

"Well, whose gonna stop me?" She smirked and backed up, giving him enough room to turn to look at her before she ran off again.

The Doctor barred his feral teeth before jumping up and sprinting after her down the long, metal corridor.

**Author's Note: Hey guys! It's me again! I'm so sorry for the late update it's been very hard to write since high school started and everyone in my house wants to use the computer. I don't know when the next chapter will be but I can assure you that I won't give up on my story.**

**I've heard some of you want River back but I don't know how to bring her back. But I can say that a certain Cyber friend is going to return soon!**

**-Chasingthestars123 :{ **


	5. Chapter 5

**Author's Note: Okay Guys, this is the day that the Doctor and Clara finally become Bonded mates! Oh, I'm so excited! I've been waiting to write this since chapter 1! Okay, okay here it goes. Concentrate. Here is chapter 5!**

**Plus, I wasn't going to bring River back it was just some readers wanted me to bring her back, but I think she is done, her story is finished. This is a Whouffle story. And I've already got a conflict planned for the couple. Let's just leave it at that.**

**Enjoy!**

After staying on the TARDIS for a few weeks reading books, playing games, and hours upon hours of teasing the Doctor, Clara decided to finally go home which caused him to panic and become strangely possessive momentarily before Clara clarified that she only wanted to visit the Maitlands, making the Doctor sigh in relief and blush as he baffled about how he knew that. When Clara was about to walk out of the TARDIS doors the Doctor grabbed her by the waist and pulled her into a passionate kiss, one involving a lot of lips smacking and tongues. Clara had to escape his grasp as he kept pulling her back into his embrace to kiss her whether on the lips, jaw, neck, collarbone, ear, and practically anything he could reach. She eventually had to force him to let go of her, making him look like a small puppy that just got kicked but quickly turned into one of giddiness as she kissed him one last time.

As the Doctor watched her walk towards the Maitlands house he had to suppress the urge to yank Clara back into the TARDIS and keep her there as his for as long as she's his mate. He had to grip the door of his precious machine, digging his finger nails into the wood. The TARDIS whined in protest as her wood was being scraped off, frantically flashing her lights to get his attention. He apologized to the old girl and locked the doors behind him to prevent his instincts from taking over. He ran over to the console and began flicking switches and turning knobs, he wanted to get to Clara as quickly as he could, he couldn't go another minute without her safe in his arms. It literally hurt to be away from her.

It starts out as an irritating itch, before turning into a burn, and then a hole in his chest. Physical Pain.

He sprints to the doors, eager to see Clara when the TARDIS stops him. The doors are locked. He looks up in concern and annoyance at the rotating spirals above the console.

"What's wrong, Sexy?" He asked impatiently.

He didn't want to see Clara, he _needed_ to see Clara. His skin burned without her touch to soothe the pain, to ease the fire of desire for her.

Sexy let out a long groan of worry, she's sensed something was wrong outside, warning him of the dangers that could be outside her doors. The Doctor could tell she was uneasy with letting him out, he gently caressed her interior wall in comfort.

"It's alright, this is Clara's house. What could be out there? Come on, I need to see Clara," He pushed on the doors.

The TARDIS gave another warning before letting him out, unlocking her doors suddenly so he stumbled a bit when he pushed once more at her double doors.

Before he could get a chance to glare at the blue box, he caught a smell. A certain smell. It smelled sweet. Very sweet. It almost smells like…

He froze, his head snapping into the direction of the Maitland's house, the source of the smell and ran towards it as fast as he could. The scent was blinding him, making him rely only on instinct. He could feel his inner Alpha taking over as he got closer to the house.

Almost there.

"Hey, Doctor!"

The Doctor stops short and looks beside him. Artie.

"Oh, hello, Artie," He tries to control himself, taking deep breaths and clutching his fists. Artie notices and his head tilts to the side in curiosity.

"Are you alright, Doctor?" He asks.

The Doctor takes another deep breath.

"Yes, absolutely! I'm always alright, call me the king of alright! No, forget that don't call me that call me the Doctor! I'm just here to pick up Clara, don't worry," He began to walk frantically up to the house, but Artie stopped him.

"Actually, Clara's not feeling so good. She told me to tell you that she can't go on an adventure with you today. Sorry, Doctor,"

"What do you mean she's not feeling good?" He turned around and studied the young boy.

"Well I heard her from upstairs and it sounded like she was whining and crying. When I went up to ask but she just said she was feeling sick and to tell you she can't go with you," He replied.

The Doctor thought.

Whining and crying. Those were symptoms of heat, yet there were also for stomach aches, too. But the smell, oh the lovely smell of an Omega's heat was in the air. The smell of it was making his hearts beat faster and faster.

Then, with his sharp Time Lord hearing he heard his Omega calling for him. Her loud yet soft cry for him, for her Alpha to come and take her. _His_ Omega. His need to mate blinds him and all he could do now was find her and take her.

Without a word the Doctor ran into the house and dashed up the stairs, the smell getting stronger and stronger. His pupils dilated and his muscles tensed up when he entered her room. Oh, it was defiantly Omega heat. Standing in the door way he could see his Clara writhing and thrashing on the bed, jeans soaked and tears rolling down her cheeks. She howled for her Alpha, sensing him in the room and surrendering her body to him, she needed him to take her. Now.

Her Alpha growled as he crossed over towards her, long powerful legs taking long strides, eager to fill her needs. The Doctor inhaled deeply when he reached her, face buried in her neck, he could already feel himself getting hard. He needed to get them out of here, back into the TARDIS. Roughly, he picked Clara up into his strong arms and ran down the stairs and to the TARDIS, he could hear Artie calling out to him but ignored the boy.

He slammed the double doors closed behind him as he entered and immediately sprinted to his bedroom. He was fully erect now and ready to take. To claim. He burst through his door, hearing it hit the wall harshly and threw Clara onto the bed. He shook his jacket off and ripped his vest from his chest, not caring about the clothing and tore his shirt from his now exposed torso. He frantically undid his belt and yanked his trousers down. His large Alpha cock sprang from his blue pin-striped pants and he climbed onto the bed, grabbing Clara by the ankles and dragging her to him, a wolfish grin on his face and teeth bared, his sharp canines ready to mark.

Clara whimpered at the size of him. He was large! Larger than she's ever had. That she's only had. She hadn't told him she was virgin, she didn't know when to bring it up! Her heat started this morning when she woke up feeling strangely aroused, her body overheating and soon pain came to play a part of her heat. She sat there for hours calling out to her Alpha, needing him to take her. But now that she's here she is scared out of her mind. She doesn't know what to do! And the smell of her Alpha's arousal made her give in, her Omega instincts began to play its part and she submitted. She laid herself on the bed, legs spread eagle wide, her heat scent filling the air as she surrendered to him.

The Doctor snarled and pounced on her, her scent filling his nostrils making him even hungrier for her. He couldn't control himself as he kneeled on top of her, legs on either side of her, hands gripping her waist hard enough to leave bruises and kissed her hard, deep and he devoured her. She once again whimpered into his mouth, tears slipping past her eyes and she begged. Begged for him.

"Doctor," She cried, "Please, I can't wait any longer. Please!"

He yelped at her, teeth snapping close to her face as a display of dominance, a low grumbling sound erupting from deep in his throat, signaling that he was in charge, he was the boss, that he was the Alpha. She coiled backed down and whined, she looked into his eyes to see all black with barely any hints of green, and she glanced down at his mouth to see it hanging open with sharp teeth bare. Sweat was already dripping from his forehead and his hair stuck to his head. His strong, veiny arms that held him up were placed on either side of her head, she could feel his breath on her neck as his face came closer. He nibbled on her flesh and tasting before biting, marking. She held back a cry, the pain shooting down between her legs and she grinded against him causing him to let out a warning snarl.

"Doctor," She whimpered.

He huffed out a breath and began to rip her clothes off. He took the fabric between his fingers and yanked, the shirt ripping apart and he threw it across the room along with her jeans. Now the only thing standing between him and his wonderfully aroused Omega was her panties. He glanced up at her before he tore it off of her and she yelped in surprise, the air making her shiver as she felt cold surround her but it was swiftly replaced with the warmth of his body flushed against hers. She whimpered when she felt his large cock soaking in his own pre-cum sandwiched between her body and his, he shifted causing Clara to moan as his member rubbed against her clit.

She could feel him lower his head to where her neck and shoulder met and nuzzled his face into her ear and felt the vibrations of the growl deep in his throat as he spoke.

"My Clara, my little Omega so wet for me," His hot breath searing her ear, "Mine. All mine, only mine. No one else's." He bucked hard against her to prove his point.

"Yes," She whispered, "Yours only."

He rumbled possessively and grabbed her waist and thrust his hips hard into hers, she cried out.

"Mine!" He forced her legs apart and straddled her before guiding his large member to her entrance, she whimpered as she felt the tip stretch her followed by the rest of his cock which was very painful considering she's never done this before.

He could see the pain on her face but he couldn't stop, he was running on Alpha instinct only and it said to take, claim, and own. Once he was fully inside her he waited for her to adjust to him before pulling out of her all the way and thrusting back in, upper lip curled dangerously into a menacing snarl. Clara had to bite her lip to keep herself from crying out as the pain slowly turned into pleasure, her hips rocking in time with his. She wrapped her legs around his waist and squeezed making him grunt. She was finally his.

The Doctor's pace increased as his desire to mate with her fueled his hearts to beat faster, he was clenching his jaw and breathing deep, her scent was palpable. He sucked and lapped at her scent glands on her neck, unable to get enough of her sweet smell. He gripped her hips holding her still, finger nails digging into her skin as he pounded into her. He looked down to see himself covered in both of their fluids, how easily he slides in and out of her, he rests his head on her shoulder and he can feel the base of his cock beginning to swell. The knot was forming, the first sign of Bonding.

His thrusts become more aggressive as his knot bulges up, making it difficult to fit in her. Clara can feel the swollen knot and screams. The base stretching her further, almost painfully as his thrusts became ragged.

She could feel herself close to the edge and cried out to her Alpha, needing him to come inside of her, to mark her as his. His name bubbled on her lips and her whole body arched back as she came. She screamed and pulled at his hair, thighs clenching around him tight and stars exploded from behind her eyelids as an electric wave of liquid pleasure flowed through her body. The Bonding taking place between them made it more powerful and she almost passed out from the intensity of it all.

Feeling his Omega come around him caused him to pound into her with greater force as he felt himself getting closer to his orgasm. His knot was almost at its full size and he knew he had to get deep inside her before he came or else the Bonding couldn't take place. He buried his face into her neck, sucking and licking to mark her but it wasn't enough. He bared his sharp canines and sank his teeth into the conjoined section of her neck and shoulder hard enough to draw blood. He licked up the red substance and swallowed, lapping his tongue against the wound and smirked. He had successfully marked her as his, permanently. He gasped when he felt himself come and grabbed Clara, yanking her whole body towards him, forcing himself and his bulge into her and spilling himself inside of her. He threw his head back to the dark ceiling in his room and roared.

"**MINE**!"

The Doctor clutched Clara close to him as he came down from his high, he jaggedly thrust into her a few more times before collapsing. They were both rasping, lungs burning for oxygen and soon laid still. His knot throbbing as loads and loads of his seed poured into her, they would be stuck like this for a while. His Alpha instinct fades and it feels like he could see clear again, he glances at Clara who has her eyes closed, her breathing has returned and her heartbeat slowly beat back to its normal rate. The Doctor carefully lifted his hand a gently caressed to bottom lip with his thumb. A small smile formed on her face and she lazily opened her eyes.

"Hello," She said.

The Doctor huffed out a laugh and smiled.

"Hello,"

Clara shifted her body to get into a more comfortable position and suddenly felt a sharp pain searing down between her legs. She looked down to see the Doctor buried deep inside her, his knot making it impossible to pull out, it locked them together while the Doctor continued to pour his seed into her. The warmth of his milt filling her made her sigh and snuggle further into him, taking in his dominating scent.

Clara no longer smelled of herself for she was covered head to toe in his scent, the whole room smelled of the powerful Alpha male laying on top of her. She nuzzled her head into his jaw, her Omega instinct made her want to please him any time of day.

The Doctor closed his eyes and sighed, smiling at her gesture and he tilted his head behind her ear and licked, his rough tongue running over her soft skin for comfort in return. He needed to make sure his new mate felt safe and protected, it was his duty as Alpha male. Clara hummed in pleasure and leaned her head away to grant him more access to her sensitive ear.

After about an hour of the Doctor grooming Clara's neck and hair line with his tongue, his knot began to deflate and he pulled out of her, juices and semen was coating his still hard cock and he shivered at being taken away from his mate's warmth. Clara whined and whimpered at the feeling of being empty and the Doctor quickly buried himself back inside her for her benefit and his.

They both laid there with the Doctor on top of Clara, both cherishing the small moments they have together. Clara's hands ruffled through the Doctor's soft brown hair, twirling some in her fingers and massaging his scalp. The Doctor rested his head against her chest and sighed happily, fingers gliding upon her soft flesh leaving goosebumps in their wake. Clara leaned forward to press a light kiss to her mate's forehead before relaxing backing into his embrace. His eyes closed momentarily as her soft lips pressed against his skin, his arms tightening themselves around her protectively with hints of possessiveness.

"So," Clara spoke quietly, "How long is this heat thing supposed to last?"

The Doctor shifted his head so it rested against her chest and looked into her dark chocolate eyes.

"Well, it normally lasts for about a few days, a week at most,"

Clara's eyes widened.

"You mean we're going to be having sex for the next week?"

"Why? Do you have a problem with that?"

"No, as long as if we can have sex like that again," Clara clenched her thighs around his rick hard member. The Doctor hissed as his cock was squeezed, his upper lip curled.

"Yep, a whole seven days of making you mine," He grinned and bared his sharp canines. Clara's eyes shot down to his teeth and quirked an eyebrow.

"You know you bit me pretty hard," She raised a hand to feel the healing wound.

Instead of feeling guilty and treating the red mark like he normally would, he grinned proudly and scanned his imprint on her.

"It's part of the Bonding between mates. The Alpha would mark his Omega by biting her until blood sheds and licking it, leaving some of his saliva inside her." He smiled, satisfied with his work.

"But I thought you can mark an Omega by covering her in his scent," She thought carefully.

"There are many different ways to mark the Omega but this one is only for Bonding. It secures the mates together for life so no else can take my Omega," He grinned once more and tightened his hold on her, snuggling his face into her sweet smelling hair.

Clara chuckled as he started talking in first person and stroked his hair.

"Your Omega," She sighed.

"My Omega," He confirmed.

A few hours later Clara felt heat starting building up in her lower stomach and looked worriedly at the Doctor.

"Doctor, I think it's starting again," She started to panic until she realized she had the Doctor here with her. She sighed in relief.

The Doctor was still inside her and his cock has been hard for the last hour. Painfully hard. He lifted himself up by his elbows and knees and pulled out of her, pleasure ran through him and he soon thrust back in. Clara's nails ran down his back as she arched up to him, once again surrendering her body to him.

The Doctor's Alpha instincts rose at the smell of Omega heat and they went through the process over and over again that day. Clara was surprised when the Doctor poured so much of his seed into her but he said no to worry about it. After all Alphas produce gallons upon gallons of semen to provide for his mate when she's in need.

**Author's Note: Hey, Guys! I really hoped you enjoyed this chapter. I'm really bad at writing smut as you can see and I tired my hardest on it. Sorry for the crappy ending! I just have so much homework and my dad said I can't use the computer until I finished, so yeah.**

**Hope to see y'all next chapter!**

**Chasingthestars123- :{**


End file.
